Annotation and Ranking of Structural Variation

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data

ClassifyCNV: a tool for clinical annotation of copy-number variants

Copy Number Variation

Copy number variant caller and depth visualization utility for PacBio HiFi reads

Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.

What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.

Integrated copy number variation detection toolset

Workflow for Sequenza, cellularity and ploidy

A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads

Short reads aligner for NIPT/CNV

This repository contains the code to run the ASCETS arm-level copy number events caller for targeted sequencing data. ASCETS produces arm-level copy-number variant calls and arm-level weighted average log2 segment means from segmented copy number data.

Official code repository for JAX-CNV

Copy number estimation of highly duplicated sequences

A fork of the project Excavator2 from sourceforge.

Dzyaloshinskii-Moriya interaction for crystallographic class Cnv

A pipeline for detecting Somatic Insertion of DE novo RETROcopies

Bioinformatics CNV Detection with Random Forest Model